Contacts of the strand formed by residues 111 - 116 (chain A) in PDB entry 6FI8
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with CYS 111 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A ILE* 5.1 0.2 - - + -
22A VAL 3.5 11.7 - - - +
23A TRP* 3.9 13.0 - - + -
78A MET* 4.4 3.4 - - - -
81A ILE* 4.0 35.0 - - + -
85A LYS* 4.5 4.3 - - - +
110A SER* 1.3 80.6 + - - +
112A PHE* 1.3 61.5 + - - +
113A ILE* 4.0 4.7 - - - -
12B ASN 3.5 1.7 + - - +
13B VAL* 3.6 27.7 - - - +
14B VAL* 3.2 23.2 + - - -
18C A 3.8 13.2 - - - -
35C T 4.9 2.7 - - - -
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Residues in contact with PHE 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A HIS* 4.3 11.9 - - - -
21A ILE* 3.3 6.2 - - - +
22A VAL* 2.7 54.7 + - + +
111A CYS* 1.3 72.9 - - - +
113A ILE* 1.3 65.8 + - - +
114A SER* 3.7 24.0 - - - -
7B TYR* 3.4 50.3 - + - -
14B VAL* 3.3 23.1 - - + -
18C A 4.1 13.2 - - + +
0E C 3.2 50.5 - + - +
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Residues in contact with ILE 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A TYR* 3.6 35.0 - - + -
20A HIS 3.4 3.8 - - - +
21A ILE* 4.8 2.5 - - + -
77A VAL* 4.3 4.9 - - + -
78A MET* 3.5 31.6 - - - -
81A ILE* 3.6 23.1 - - + -
111A CYS* 4.0 2.9 - - - -
112A PHE* 1.3 84.6 - - - +
114A SER* 1.3 65.8 + - - +
13B VAL* 3.8 16.8 - - + -
14B VAL 3.0 6.1 + - - +
15B TYR* 3.1 13.7 - - + -
16B SER 3.0 22.7 + - - -
17B CYS* 3.8 13.0 - - - -
73B PRO* 4.1 9.0 - - + -
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Residues in contact with SER 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A TYR* 4.5 1.6 - - - -
20A HIS* 2.7 47.3 + - - +
112A PHE* 3.7 23.6 - - - -
113A ILE* 1.3 79.4 - - - +
115A THR* 1.3 69.2 + - - +
116A VAL* 3.6 1.5 - - - +
7B TYR* 4.3 8.2 + - - -
16B SER* 3.3 16.6 + - - -
117B GLY* 5.4 2.1 - - - -
118B GLY 5.7 0.9 + - - -
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Residues in contact with THR 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A LYS 3.5 4.0 - - - -
19A TYR* 3.7 20.6 - - + +
114A SER* 1.3 78.9 + - - +
116A VAL* 1.3 62.6 + - - +
16B SER* 2.9 10.0 + - - -
17B CYS* 3.5 21.7 - - + -
18B LYS* 2.9 18.9 + - - +
19B TYR* 4.3 2.2 - - + -
115B THR* 3.6 30.1 - - + -
116B VAL 2.7 24.5 + - - -
117B GLY* 3.2 22.3 - - - -
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Residues in contact with VAL 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A LYS* 2.8 23.3 + - + +
20A HIS* 3.9 20.4 - - + +
68A LEU* 4.3 8.1 - - + -
114A SER* 3.6 13.0 - - - +
115A THR* 1.3 81.6 - - - +
117A GLY* 1.3 63.2 + - - +
115B THR* 2.8 22.5 + - - -
117B GLY* 4.1 3.4 - - - +
119B ALA 4.2 4.0 - - - +
121B LEU* 3.7 38.1 - - + +
124B VAL* 3.9 28.0 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il